name about category URL
3dslicer multi-platform, free and open source software package for visualization and medical image computing Graphics https://www.slicer.org
454 sequencing data analysis software Bioinformatics http://454.com
R free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
a2ps any to postscript System Tools http://www.gnu.org/software/a2ps
abaqus finite element analysis Physics http://www.3ds.com
abyss de nono sequence assembler intended for short paired-end reads and large genomes Bioinformatics http://github.com/bcgsc/abyss
adapterremoval rapid adapter trimming, identification, and read merging Bioinformatics http://github.com/MikkelSchubert/adapterremoval
ale Assembly Likelihood Estimator Bioinformatics http://github.com/sc932/ALE
aligngraph Algorithm for secondary de novo genome assembly guided by closely related references Bioinformatics http://github.com/baoe/AlignGraph
allpathslg high quality genome assembly from low cost data Bioinformatics http://broadinstitute.org/software/allpaths-lg/blog
amber assisted model building with energy refinement Molecular Biology http://ambermd.org
amira a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities Graphics http://www.vsg3d.com/amira
anaconda scientific python distribution Programming Tools http://continuum.io
anaconda3 scientific python distribution Programming Tools http://continuum.io
analysis evolutionary genetic analysis Bioinformatics http://molpopgen.org
ant Java Library and Command Line Tool for building packages Programming Tools http://ant.apache.org
ants Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging Libraries http://picsl.upenn.edu/software/ants/
arden2bytecode language to represent medical knowledge Bioinformatics http://arden2bytecode.sourceforge.net
arem peak caller for ChIP-Seq experiments that robustly handles short readds with multiple possible mappings Bioinformatics http://sourceforce.net/projects/arem
argparse argparse Libraries http://www.python.org
armadillo C++ linear algebra library Libraries http://arma.sourceforge.net
arpack collection of Fortran77 subroutines designed to solve large scale eigenvalue problems Libraries http://www.caam.rice.edu/software/ARPACK
arrayfire ArrayFire is a high-performance software library designed for maximum productivity and speed without the hassle of writing difficult low-level device code. Libraries http://arrayfire.com
ase Atomistic Simulation Environment Molecular Biology https://wiki.fysik.dtu.dk/ase/overview.html
aspera high performance file transfer Accessories http://asperasoft.com
astrobear Collection of libraries used by astrobear Libraries http://astrobear.pas.rochester.edu
astropy community python library for astronomy Physics http://www.astropy.org
atk accessibility toolkit Libraries http://ftp.gnome.org/pub/gnome/sources/atk
atlas automatically tuned linear algebra software Mathematics http://sourceforge.net/projects/math-atlas
audacity audio editor Accessories http://audacityteam.org
autoconf generate configure scripts Programming Tools http://www.gnu.org/software/autoconf
autodockvina molecular docking and virtual screening Molecular Biology http://vina.scripps.edu
automake generate Makefile.in files Programming Tools http://www.gnu.org/software/automake
avogadro molecule editor and visualizer Chemistry http://avogadro.cc
bali-phy bayesian alignment and phylogeny estimation Bioinformatics http://www.bali-phy.org
bam2x extract info from bam files Bioinformatics http://github.com/nimezhu/bam2x
bamtools API and command line toolkit for working with BAM data Bioinformatics http://github.com/pezmaster31/bamtools
basespace-cli BaseSpace Sequence Hub Bioinformatics http://basespace.illumina.com
bazel build tool Programming Tools http://bazel.io
bbcp file transfer client Internet http://www.slac.stanford.edu/~abh/bbcp
bbmap BBMap short read aligned and other bioinformatic tools Bioinformatics http://sourceforge.net/projects/bbmap
bcftools program for variant calling and manipulating VCFs and BCFs Bioinformatics https://github.com/samtools/bcftools/wiki
bcl2fastq bcl conversion and multiplexing Bioinformatics http://www.illumina.com
beacon automated tool for Bacterial gEnome Annotation ComparisON Bioinformatics http://www.cbrc.kaust.edu.sa/BEACON
bear2fix Routines for analyzing hdf5 files produced by astrobear Physics http://astrobear.pas.rochester.edu
beast2 Bayesian Evolutionary Analysis by Sampling Trees Bioinformatics http://beast2.org
bedops fast, highly scalable and easily-parallelizable genome analysis toolkit Bioinformatics http://bedops.readthedocs.io
bedtools genome arithmetic suite Bioinformatics http://bedtools.readthedocs.org
bfast Blat-like Fast Accurate Search Tool Bioinformatics http://sourceforge.net/projects/bfast
bioformats Tools for manipulating open microscopy formats Libraries http://openmicroscopy.org
biom-format a general-use format for representing biological sample by observation contingency tables Bioinformatics http://biom-format.org
bioperl Perl code useful in biology Bioinformatics http://www.bioperl.org
biopython tools for biological computation Libraries http://biopython.org
bioxtasraw analysis of small angle x-ray scattering data Chemistry http://sourceforge.net/projects/bioxtasraw/b1
bismark bisulfite read mapper and methylation caller Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/bismark
bison General-purpose parser generator Libraries http://www.gnu.org/software/bison/
blas Basic Linear Algebra Subprograms Libraries http://www.netlib.org/blas/
blasr PacBio long read aligner Bioinformatics http://github.com/PacificBiosciences/blasr
blast basic local alignment search tool Bioinformatics http://blast.ncbi.nlm.nih.gov
blat BLAST-like alignment tool Bioinformatics http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/blat/
bonnie benchmark suite System Tools http://coker.com.au/bonnie++
boost portable C++ source libraries Libraries http://www.boost.org
bowtie ultrafast memory-efficient short read aligner Bioinformatics http://bowtie-bio.sourceforge.net
bowtie2 ultrafast memory-efficient short read aligner Bioinformatics http://bowtie-bio.sourceforge.net/bowtie2
breakdancer genome-wide detection of structural variants from next generation paired-end sequencing reads Bioinformatics http://sourceforge.net/projects/breakdancer/
brownie reference based error correction Bioinformatics http://github.com/biointec/brownie
bwa Burrows-Wheeler aligner Bioinformatics http://bio-bwa.sourceforge.net
bwidget TCL widget library Programming Tools http://core.tcl.tk/bwidget
bwtool command-line utility for bigWig files Bioinformatics http://github.com/CRG-Barcelona/bwtool
bzip2 compression System Tools http://bzip.org
caffe deep learning framework Computer Science http://caffe.berkeleyvision.org
cairo 2D graphics library with support for multiple output devices Libraries http://cairographics.org
canu fork of Celera Assembler, designed for high-noise single-molecule sequencing Bioinformatics http://github.com/marbl/canu
catdoc read MS Word and Excel files Accessories http://www.wagner.pp.ru/~vitus/software/catdoc
cdec decoder, aligner, and learning framework for statistical machine translation and similar prediction models Computer Science http://cdec-decoder.org
cdo Climate Data Operators Physics http://code.zmaw.de/projects/cdo
ceas cis-regulatory element annotation system Bioinformatics http://liulab.dfci.harvard.edu/CEAS
cgal Computational Geometry Algorithms Library Libraries http://www.cgal.org
chimera visualization of molecular structures Chemistry http://www.cgl.ucsf.edu/chimera
circos circular genome variation and data visualization tool Graphics http://circos.ca
cisa contig integrator for sequence assembly Bioinformatics http://sb.nhri.org.tw/CISA
cistrome platform for transcriptional regulation studies Bioinformatics http://bitbucket.org/cistrome/cistrome-applications-harvard/src
clapack f2c'd version of LAPACK Libraries http://www.netlib.org/clapack
clustalw multiple sequence alignment Bioinformatics http://clustal.org
clustalx multiple sequence alignment Bioinformatics http://clustal.org
cmake an extensible, open-source system that manages the build process in an operating system System Tools http://www.cmake.org
commet COmpare Multiple METagenomes Bioinformatics http://colibread.inria.fr/software/commet
comsol multiphysics simulation Physics http://www.comsol.com
conifer copy number inference from exome reads Bioinformatics http://conifer.sourceforge.net
convert ImageMagick Convert utility System Tools http://www.imagemagick.org
corenlp Java viewer for chemical structures in 3D Chemistry https://stanfordnlp.github.io/CoreNLP/cmdline.html
corset clustering de novo assembled transcripts and counting overlapping reads Bioinformatics http://github.com/Oshlack/Corset
cp2k program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems Chemistry http://www.cp2k.org
cpc Coding Potential Calculator Bioinformatics http://cpc.cbi.pku.edu.cn
cpmd Car-Parrinello Molecular Dynamics Chemistry http://www.cpmd.org
crisp code for multi-sample variant calling from sequence data Bioinformatics http://github.com/vibansal/crisp
crispresso analysis of CRISPR-Cas9 genome editing outcomes from sequencing data Bioinformatics http://github.com/lucapinello/CRISPResso
ctm C implementation of the correlated topic model (CTM) Mathematics http://www.cs.princeton.edu/~blei/ctm-c/
cuda CUDA Software Development Kit (gcc 4.4.7) Programming Tools https://developer.nvidia.com/cuda-zone
cudamat Python module for performing basic dense linear algebra computations on the CPU using CUDA Libraries http://github.com/cudamat/cudamat
cudnn GPU-accelerated library for deep neural networks Programming Tools http://nvidia.com
cufflinks transcript assembly, differential expression, and differential regulation for RNA-Seq Bioinformatics http://cufflinks.cbcb.umd.edu
curl multiprotocol file transfer library Internet http://curl.haxx.se/libcurl
cushaw gapped short-read alignment Bioinformatics http://cushaw3.sourceforge.net
cutadapt removes adapter sequences from DNA sequencing reads Bioinformatics http://github.com/marcelm/cutadapt
cytoscape network visualization Graphics http://www.cytoscape.org
db Berkeley DB Libraries http://www.oracle.com/technetwork/database/database-technologies/berkeleydb/overview/index.html
dbg2olc assembly of large genomes using long erroneous reads of the third generation sequencing technologies Bioinformatics http://github.com/yechengxi/DBG2OLC
dcs client application designed to be run locally on a data producer's machine System Tools http://scm.dataconservancy.org
ddimap DDiMap Bioinformatics https://github.com/jpspence/DDiMAPpublic
dealii open source finite element library Libraries http://dealii.org
deeptools tools for exploring deep sequencing data Bioinformatics http://deeptools.readthedocs.io
dendropy phylogenetic computing Bioinformatics http://pythonhosted.org/DendroPy
device advanced, finite element multiphysics simulation environment Physics http://www.lumerical.com
dftb fast approximate DFT for molecules Chemistry http://www.scm.com
diffsplice genome-wide detection of differential splicing events with RNA-seq Bioinformatics http://www.netlab.uky.edu/p/bioinfo/DiffSplice
digits Deep Learning GPU Training System Computer Science http://github.com/NVIDIA/DIGITS
disperse Automatic identification of persistent structures Mathematics http://www2.iap.fr/users/sousbie/web/html/indexd41d.html?
dock molecular docking Chemistry http://dock.compbio.ucsf.edu
dofe distribution of fitness effects and rates of adaptive substitution Bioinformatics http://www.lifesci.susx.ac.uk/home/Adam_Eyre-Walker/Website/Software.html
dptools Processing and converting data related to the DFTB+ package Chemistry http://www.dftb-plus.info/tools/dptools
drmaa-slurm DRMAA for Slurm Libraries http://apps.man.poznan.pl/trac/slurm-drmaa
duc File usage analyzer System Tools https://duc.zevv.nl
ea-utils Command-line tools for processing biological sequencing data Libraries https://code.google.com/p/ea-utils/
eclipse integrated development environment Programming Tools http://eclipse.org
eigen C++ template library for linear algebra Libraries http://eigen.tuxfamily.org
elan annotations on video and audio resources Computer Science http://tla.mpi.nl/tools/tla-tools/elan
elfutils collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux Programming Tools http://sourceware.org/elfutils
emacs extensible, customizable text editor Accessories http://www.gnu.org/software/emacs
emboss European Molecular Biology Open Software Suite Bioinformatics http://emboss.sourceforge.net
ensembl-tools variant effect predictor Bioinformatics http://useast.ensembl.org
epstool Epstool is a utility to create or extract preview images in EPS files, fix bounding boxes and convert to bitmaps Accessories http://pages.cs.wisc.edu/~ghost/gsview/epstool.htm
exabayes bayesian tree inference Bioinformatics http://sco.h-its.org/exelixis/web/software/exabayes
examl Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI Bioinformatics http://github.com/stamatak/ExaML
exonerate a generic tool for pairwise sequence comparison Libraries http://www.ebi.ac.uk/~guy/exonerate/
expat Expat XML parser Libraries http://expat.sourceforge.net
expect automate interactive applications System Tools http://expect.sourceforge.net
express streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences Bioinformatics http://bio.math.berkeley.edu/eXpress/overview.html
falcon experimental PacBio diploid assembler Bioinformatics http://github.com/PacificBiosciences/falcon
fastqc quality control tool for high throughput sequence data Bioinformatics http://www.bioinformatics.babraham.ac.uk/projects/fastqc
fastx FASTQ/A short-reads pre-processing tools Bioinformatics http://hannlab.cshl.edu/fastx_toolkit
fdtd-solutions Single and multi-processor finite-difference time-domain optical design Physics http://www.lumerical.com
fenics solution of differential equations Mathematics http://fenicsproject.org
ferret visualization and analysis environment for studying climate Graphics http://ferret.pmel.noaa.gov
ffi portable, high level programming interface to various calling conventions Libraries http://sourceware.org/libffi
ffmpeg A complete, cross-platform solution to record, convert and stream audio and video Graphics http://www.ffmpeg.org
fftw2 FFTW library for computing the discrete Fourier transform (DFT) Libraries http://www.fftw.org/
fftw3 FFTW3 library for computing the discrete Fourier transform (DFT) Libraries http://www.fftw.org/
figtree molecular evolution, phylogenetics, and epidemiology Bioinformatics http://tree.bio.ed.ac.uk
fiji Fiji is just ImageJ with plugins Graphics http://fiji.sc
findutils basic directory searchiing utilities System Tools http://gnu.org/software/findutils
firefox web browser Internet http://www.mozilla.org/Firefox
flash merge mates from fragments that are shorter than twice the read length Bioinformatics http://sourceforge.net/projects/flashpage
flens flexible library for efficient numerical solutions Mathematics http://flens.sourceforge.net
flex the fast lexical analyser Libraries http://sourceforge.net/projects/flex/
flowgate free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
fltk a cross-platform C++ GUI toolkit Libraries http://www.fltk.org
freebayes Bayesian haplotype-based polymorphism discovery and genotyping Bioinformatics http://github.com/ekg/freebayes
freeglut OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library Libraries http://freeglut.sourceforge.net
freesurfer processing and analyzing brain MRI images Graphics http://surfer.nmr.mgh.harvard.edu
freetype freely available software library to render fonts Libraries http://www.freetype.org
freexl library to extract valid data from within an Excel spreadsheet Libraries http://www.gaia-gis.it/fossil/freexl/index
fsl analysis tools for FMRI, MRI, and DTI brain imaging data Bioinformatics http://fsl.fmrib.ox.ac.uk
gam-ngs genomic assemblies merger for NGS Bioinformatics http://github.com/vice87/gam-ngs
gamess general atomic and molecular electronic structure system Chemistry http://www.msg.ameslab.gov/gamess
gap2seq filling gaps in scaffolds produced by genome assembly tools Bioinformatics http://www.cs.helsinki.fi/u/lmsalmel/Gap2Seq
gapfiller close gaps produced by a scaffolding program using one or more mate pairs or paired-end libraries Bioinformatics http://baseclear.com
gatb Genome Assembly Tool Box Bioinformatics http://gatb-core.gforge.inria.fr
gatk genome analysis toolkit Bioinformatics http://www.broadinstitute.org/gatk
gaussian quantum chemistry Chemistry http://www.gaussian.com
gcc GNU compiler collection Programming Tools http://gcc.gnu.org
gcta genome-wide complex trait analysis Bioinformatics http://cnsgenomics.com
gdal translator library for raster and vector geospatial data formats Physics http://www.gdal.org
gdc-client GDC data transfer tool Accessories http://github.com/NCI-GDC/gdc-client
gdk-pixbuf toolkit for image loading and pixel buffer manipulation Libraries http://ftp.gnome.org/pub/gnome/
gem5 modular platform for computer system architecture research Programming Tools http://www.gem5.org
geneious bioinformatics tools Bioinformatics http://geneious.com
genepattern computational biology open-source package Bioinformatics http://www.genepattern.org
genetorrent downloading sequence data Bioinformatics http://www.cghub.ucsc.edu/software
genometools open source genome analysis software Bioinformatics http://genometools.org
geos geometry engine, open source Graphics http://trac.osgeo.org/geos
gephi open graph viz platform Graphics http://gephi.github.io
gffcompare classify, merge, tracking, and annotation of GFF files by comparing to a reference annotation GFF Bioinformatics http://github.com/gpertea/gffcompare
gflags command line flags processing Programming Tools http://github.com/gflags
ghc Glasgow Haskell Compiler Programming Tools http://www.haskell.org/haskellwiki/GHC
ghostscript Interpreter for the PostScript language and for PDF Graphics http://www.ghostscript.com
git distributed version control system Programming Tools http://git-scm.com
git-lfs Git large file storage Programming Tools http://git-lfs.github.com
gl2ps an OpenGL to PostScript printing library Libraries http://www.geuz.org/gl2ps/
glew OpenGL Extension Wrangler Library Libraries http://glew.sourceforge.net
glfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries http://www.glfw.org
glib a low-level libraries useful for providing data structure handling for C Libraries http://www.linuxfromscratch.org/blfs/view/svn/general/glib2.html
glibc GNU C library Libraries http://www.gnu.org/s/libc
glog google logging module Programming Tools http://github.com/glog
glpk GNU Linear Programming Kit Libraries http://www.gnu.org/software/glpk/
gmap a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics http://research-pub.gene.com/gmap
gmp GNU Multiple Precision Arithmetic Library Libraries http://gmplib.org
gmt Generic Mapping Tools: open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets Physics http://gmt.soest.hawaii.edu
gnat GNU Ada compiler Programming Tools http://libre.adacore.com
gnumpy Python interface to GPUs and numpy Libraries http://www.cs.toronto.edu/~tijmen/gnumpy.html
gnuplot plotting program Graphics http://www.gnuplot.info
gnutls secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them Libraries http://gnutls.org
gobject-instrospection middleware layer between C libraries (using GObject) and language bindings Libraries https://wiki.gnome.org/action/show/Projects/GObjectIntrospection
gpaw density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE) Molecular Biology https://wiki.fysik.dtu.dk/gpaw
gperf perfect hash function generator System Tools http://www.gnu.org/software/gperf/
gpfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries http://www.glfw.org
grace WYSIWYG 2D plotting tool Graphics http://plasma-gate.weizmann.ac.il/Grace
graphiz open source graph visualization software Graphics http://www.graphviz.org/
graphlan circular representations of taxonomic and phylogenetic trees Bioinformatics http://bitbucket.org/nsegata/graphlan
gromacs molecular dynamics Molecular Biology http://www.gromacs.org
gromacswrapper python package that wraps system calls to Gromacs tools into thin classes Chemistry http://github.com/Becksteinlab/GromacsWrapper
gshrimp image processing Data Analysis http://people.physics.illinois.edu/Selvin/PRS/students/group.html
gsl GNU scientific library Libraries http://www.gnu.org/s/gsl
gstreamer library for constructing graphs of media-handling components Libraries http://gstreamer.freedesktop.org/
gstreamer-plugins gstreamer Libraries http://notavailable.com
gtk Gimp Toolkit:A multi-platform toolkit for creating graphical user interfaces Libraries http://www.gtk.org
guile GNU Ubiquitous Intelligent Language for Extensions Programming Tools http://www.gnu.org/software/guile/
gurobi optimizer Mathematics http://www.gurobi.com
h5py HDF5 for Python Libraries http://www.h5py.org
h5utils set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format Libraries http://ab-initio.mit.edu/wiki/index.php/H5utils
hal hierarchical alignment format Bioinformatics http://github.com/glennhickey/hal
harfbuzz an OpenType text shaping engine Libraries http://www.freedesktop.org/software/harfbuzz/release/harfbuzz-0.9.27.tar.bz2
harminv a free program (and accompanying library) to solve the problem of harmonic inversion Mathematics http://ab-initio.mit.edu/wiki/index.php/Harminv
hdf4 a library and multi-object file format for storing and managing data between machines Libraries http://www.hdfgroup.org/products/hdf4/
hdf5 data model, library, file format Libraries http://www.hdfgroup.org
hdfview HDF file viewer System Tools http://www.hdfgroup.org/products/java/release/download.html
hg Mercurial Revision Control System System Tools http://mercurial.selenic.com
hisat graph-based alignment of next generation sequencing reads to a population of genomes Bioinformatics http://ccb.jhu.edu/software/hisat2
hmmer biosequence analysis using profile hidden Markov models Bioinformatics http://hmmer.org
homer motif discovery and next-gen sequencing analysis Bioinformatics http://homer.salk.edu
hoomd General purpose particle simulation toolkit Libraries http://codeblue.umich.edu/hoomd-blue
hpctoolkit High performance computing toolkit Programming Tools http://hpctoolkit.org
hpctraceviewer GUI for hpctoolkit Programming Tools http://hpctoolkit.org
hpcviewer GUI for hpctoolkit Programming Tools http://hpctoolkit.org
htseq analysis of high-throughput sequencing data Bioinformatics http://www-huber/embl.de/users/anders/HTseq/doc/overview.html
htslib library for reading/writing high-throughput sequencing data Bioinformatics http://www.htslib.org
hyphy hypothesis testing using phylogenies Bioinformatics http://github.com/veg/hyphy
hypre a library for solving large, sparse linear systems of equations on massively parallel computers Libraries http://computation.llnl.gov/casc/hypre/software.html
idl scientific programming language Data Analysis http://exelisvis.com
idp isoform detection and prediction Bioinformatics http://www.healthcare.uiowa.edu/labs/au/IDP
igv integrative genomics viewer Bioinformatics http://www.broadinstitute.org/igv
ilmbase Industrial Light & Magic base libraries Libraries http://www.openexr.com
imagemagick image processing Libraries http://imagemagick.org
impi Intel MPI Programming Tools http://software.intel.com/en-us/intel-compilers
impute genotype imputation and haplotype phasing Bioinformatics http://mathgen.stats.ox.ac.uk/impute/impute_v2.html
imsl mathematical and statistical functions Libraries http://www.roguewave.com
infernal Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities Bioinformatics http://infernal.janelia.org
inkscape A powerful, free design tool Graphics http://inkspace.org
intel Intel utilities Programming Tools http://software.intel.com/en-us/intel-compilers
intelpython intel python Programming Tools http://software.intel.com/en-us/intel-compilers
intelpython3 intel python Programming Tools http://software.intel.com/en-us/intel-compilers
iozone filesystem benchmarking System Tools http://iozone.org
ipm integrated performance modeling Programming Tools http://ipm-hpc.sourceforge.net
ipyrad Interactive assembly and analysis of RAD-seq data sets Bioinformatics http://github.com/dereneaton/ipyrad
ipython Interactive Python Programming Tools http://www.python.org
iqtree phylogenomics by maximum likelihood Bioinformatics http://iqtree.org
itk open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis Libraries http://itk.org
j3d java 3D library Libraries http://java3d.java.net
jabba read error correction tool for PacBio data Bioinformatics http://github.com/biointec/jabba
jags Just Another Gibbs Sampler Data Analysis http://mcmc-jags.sourceforge.net
jamg just annotate my genome Bioinformatics http://jamg.sourceforge.net
japsa Just Another JAva Package for Sequence Analysis Bioinformatics http://github.com/mdcao/japsa
jasper Open source JPEG-2000 part 1 codec Graphics http://www.ece.uvic.ca/~frodo/jasper/
java Java pre-release development kit Programming Tools http://www.java.com
jdk Java development kit Programming Tools http://www.java.com
jellyfish fast parallel k-mer counting for DNA Bioinformatics http://www.cbcb.umd.edu/software/jellyfish
jmol Java viewer for chemical structures in 3D Chemistry http://jmol.org
jpeg free library for JPEG image compression Libraries http://www.ijg.org/
jre Java pre-release development kit Programming Tools http://www.java.com
jruby ruby programming language on the Java virtual machine Programming Tools http://jruby.org
julia high-level, high-performance dynamic programming language Programming Tools http://julialang.org
jupyter Interactive Python Programming Tools http://www.python.org
jupyterhub multiuser version of the notebook designed for centralized deployments in companies, university classrooms and research labs Programming Tools https://github.com/jupyterhub/jupyterhub
kallisto program for quantifying abundances of transcripts from RNA-Seq data Bioinformatics http://pachterlab.github.io/kallisto
karect KAUST assembly read error correction tool Bioinformatics http://github.com/aminallam/karect
kenlm estimates, filters, and queries language models Libraries https://kheafield.com/code/kenlm/
kentutils UCSC command line bioinformatics utilities Bioinformatics http://github.com/ENCODE-DCC/kentUtils
khmer nucleotide sequence k-mer counting, filtering, graph traversal Bioinformatics http://github.com/dib-lab/khmer
lammps molecular dynamics Chemistry http://lammps.sandia.gov
lapack linear algebra package Libraries http://www.netlib.org/lapack
last genome-scale sequence comparison Bioinformatics http://last.cbrc.jp
latex2html bringing high quality documents to the web Accessories http://www.latex2html.org
lcms littlc cms color engine Libraries https://sourceforge.net/projects/lcms/files/
leveldb lightweight single purpose library for persistence with bindings Data Analysis http://leveldb.org
lftp sophisticated ftp/http client, and a file transfer program supporting a number of network protocols System Tools http://lftp.yar.ru
libav a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts Libraries https://libav.org/download.html
libcanberra implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME Libraries http://0pointer.de/lennart/projects/libcanberra/
libctl Guile-based library implementing flexible control files for scientific simulations Libraries http://ab-initio.mit.edu/wiki/index.php/Libctl
libevent The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached Libraries http://libevent.org
libffi Foreign Function Interface Libraries http://sourceware.org/libffi
libgd open source code library for the dynamic creation of images by programmers Libraries http://libgd.bitbucket.org
libglew The OpenGL Extension Wrangler Library Libraries http://glew.sourceforge.net
libgpuarray library to manipulate tensors on the GPU Libraries http://github.com/Theano/libgpuarray
libjpeg-turbo JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression Libraries http://sourceforge.net/projects/libjpeg-turbo/files/1.3.1/
libmatheval parse and evaluate symbolic expressions input as text Libraries http://gnu.org
libogg a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs Libraries https://www.xiph.org/downloads/
libpng the free reference library for reading and writing PNGs Libraries http://www.libpng.org
libreoffice free office suite Accessories http://libreoffice.org
libsequence C++ class library for evolutionary genetic analysis Bioinformatics http://github.com/molpopgen/libsequence
libsndfile library for reading files containing sampled sound Libraries http://www.mega-nerd.com/libsndfile
libtasn1 ASN.1 library used by GnuTLS, GNU Shishi Libraries http://ftp.gnu.org/gnu/libtasn1/
libtool The GNU Portable Library Tool Libraries http://www.gnu.org/software/libtool/libtool.html
libunwind unwinding library Programming Tools http://github.com/pathscale/libunwind
libvorbis reference implementation of the Vorbis codec Libraries https://www.xiph.org/downloads/
libxc exchange-correlation functionals for density functional theory Chemistry http://www.tddft.org/programs/octopus/wiki/index.php/Libxc
libzip C library for reading, creating, and modifying zip archives Libraries http://www.nih.at/libzip
liggghts discrete element method particle simulation code Physics http://cfdem.com
links long interval nucleotide K-mer scaffolder Bioinformatics http://github.com/warrenlr/LINKS
lmdb lightning memory-mapped database manager Data Analysis http://lmdb.tech
locarna global and local alignment of RNA Bioinformatics http://www.bioinf.uni-freiburg.de/Software/LocARNA
loos lightweight object-oriented structure library Molecular Biology http://loos.sourceforge.net
lordec hybrid error correction program for long PacBio reads Bioinformatics http://atgc-montpellier.fr/lordec
lpp pre- and post-processing capability for the LAMMPS molecular dynamics package Physics http://www.cs.sandia.gov/~sjplimp/lammps.html
lsc long range error correction tool Bioinformatics http://www.healthcare.uiowa.edu/labs/au/LSC
luajit just-in-time compiler for lua Programming Tools http://luajit.org
lumpy a general probabilistic framework for structural variant discovery Bioinformatics http://github.com/arq5x/lumpy-sv
lxtask Lightweight X Task manager System Tools http://sourceforge.net/projects/lxde/files/LXTask
m4 Unix Macro Processor Libraries https://www.gnu.org/software/m4/
macs model-based analysis for ChIP-Seq Bioinformatics http://liulab.dfci.harvard.edu/MACS
magma GPU accelerated linear algebra Libraries http://developer.nvidia.com/magma
magmaca MAGMA computer algebra system Mathematics http://magma.maths.usyd.edu.au
maker genome annotation pipeline Bioinformatics http://www.yandell-lab.org/software/maker.html
marginalign UCSC Nanopore Bioinformatics http://github.com/benedictpaten/marginAlign
masurca whole genome assembly Bioinformatics http://www.genome.umd.edu/masurca.html
mathematica computation, symbolic mathematics, and visualization Mathematics http://www.wolfram.com
matlab MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language Mathematics http://www.mathworks.com/products/matlab/
matlab-runtime matlab runtime environment Mathematics http://www.mathworks.com
matplotlib python 2D plotting library Libraries http://matplotlib.org
mc Midnight Commander System Tools http://midnight-commander.org
md5deep compute checksums on arbitrary number of files Accessories http://md5deep.sourceforge.net
mdbtools work with files from Microsoft Access Libraries http://mdbtools.sourceforge.net
meep a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems Physics http://ab-initio.mit.edu/wiki/index.php/Meep
mega molecular evolutionary genetics analysis Bioinformatics http://www.megasoftware.net
megahit ultra-fast single-node solution for large and complex metagenomics assembly Bioinformatics http://github.com/voutcn/megahit
meld visual diff and merge tool Programming Tools http://meldmerge.org
meme fast parallel k-mer counting for DNA Bioinformatics http://www.cbcb.umd.edu/software/jellyfish
mesa 3D graphics library Libraries http://mesa3d.org
metabat tool for accurately reconstructing single genomes from complex microbial communities Bioinformatics http://bitbucket.org/berkeleylab/metabat
mfold RNA secondary structure prediction Molecular Biology http://mfold.rna.albany.edu
mgiza A word alignment tool based on famous GIZA++, extended to support multi-threading, resume training and incremental training Computer Science https://github.com/moses-smt/mgiza
mgltools Molecular Graphics Library Tools Molecular Biology http://mgltools.scripps.edu
mgtaxa taxonomic classification of metagenomic sequences with machine learning Bioinformatics http://andreyto.github.io/mgtaxa
miniasm ultrafast de novo assembly for long noisy reads (though having no consensus step) Bioinformatics http://github.com/lh3/miniasm
minimap experimental tool to find approximate mapping positions between long sequences Bioinformatics http://github.com/lh3/minimap
misopy mixture of isoforms module for isoform quantification using RNA-Seq Bioinformatics http://pypi.pyhon/org/pypi/misopy
mitoprot prediction of mitochondrial targeting sequences Bioinformatics http://ihg.gsf.de/ihg/mitoprot.html
mkl-boost MKL boost Libraries http://software.intel.com
molcas ab initio quantum chemistry software package Chemistry http://www.molcas.org
molden pre and post processing program for molecular and electronic structure Chemistry http://www.cmbi.ru.nl/molden
molstat a collection of tools for simulating and understanding single molecule behavior Chemistry http://bitbucket.org/mgreuter/molstat
mongodb cross-platform document-oriented NoSQL database Data Analysis http://www.mongodb.org
moose multiphysics object-oriented simulation environment Physics http://mooseframework.com
mopac semiempirical quantum chemistry Chemistry http://openmopac.net
mosh remote terminal application allowing roaming, intermittent connectivity, local echo Internet http://mosh.mit.edu
mpb MIT photonic bands Physics http://ab-initio.mit.edu/wiki/index.php/MIT_Photonic_Bands
mpc C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result Libraries http://www.multiprecision.org
mpfr multiple precision floating point library Libraries http://www.mpfr.org
mpiblast freely available, open- Libraries http://www.mpiblast.org/
mpich high performance and widely portably implementation of the Message Passing Interface standard Programming Tools http://www.mpich.org
mpip lightweight, scalable MPI profiling Programming Tools http://ipm-hpc.sourceforge.net
mplus latent variable modeling program Data Analysis http://statmodel.com
mrbayes bayesian inference of phylogeny Bioinformatics http://mrbayes.sourceforge.net
multiqc aggregate results from bioinformatics analyses across many samples into a single report Bioinformatics http://github.com/ewels/MultiQC
mummer modular system for rapid whole genome alignment of finished or draft sequence Bioinformatics http://sourceforge.net/projects/mummer
muscle multiple sequence alignment Bioinformatics http://www.drive5.com/muscle
mysql open source relational database management system Data Analysis http://www.mysql.com
mysql-python interface for connecting to a MySQL database server from Python Libraries http://sourceforge.net/projects/mysql-python/
mysql-workbench integrated tools environment for MySQL Data Analysis http://dev.mysql.com
namd scalable molecular dynamics Molecular Biology http://www.ks.uiuc.edu/Research/namd
nanocorr error correction for Oxford Nanopore data Bioinformatics http://github.com/jgurtowski/nanocorr
nanopolish Signal-level algorithms for MinION data Bioinformatics http://github.com/jts/nanopolish
nas hybrid approach to take advantage of data generated using MinION device Bioinformatics http://github.com/institut-de-genomique/NaS
ncftp FTP client System Tools http://ncftp.com
ncl NCAR command language Physics http://ncl.ucar.edu
nco NetCDF command operators Programming Tools http://nco.sourceforge.net
netcdf software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries http://www.unidata.ucar.edu/netcdf
netcdf-fortran software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries http://www.unidata.ucar.edu/netcdf
netlogo multi-agent programmable modeling environment Programming Tools http://ccl.northwestern.edu/netlogo
nettle cryptographic library that is designed to fit easily in more or less any context Libraries https://ftp.gnu.org/gnu/nettle/
nlopt nonlinear optimization Libraries http://ab-initio.mit.edu/wiki/index.php/NLopt
nodejs Event-driven I/O server-side JavaScript environment based on V8 System Tools http://nodejs.org
novocraft aligner for single-end and paired-end reads Bioinformatics http://www.novocraft.org
numpy fundamental package for scientific computing with Python Libraries http://www.numpy.org/
nupic hierarchical temporary memory Data Analysis http://numenta.org
nwchem quantum chemistry Chemistry http://www.nwchem-sw.org
ocaml OCAML programming language Programming Tools http://ocaml.org
ocproxy OpenConnect proxy Internet http://github.com/cernekee/ocproxy
octave high-level interpreted language, primarily intended for numerical computations Mathematics https://www.gnu.org/software/octave/
octopus density functional theory Chemistry http://www.tddft.org/programs/octopus/wiki/index.php/Main_Page
omero OMERO is client-server software for visualization, management and analysis of biological microscope images. Microscopy https://www.openmicroscopy.org/site/products/omero
opacplot python package for manipulating Equation of State and Opacity data Chemistry http://github.com/tzeferacos/opacplot_deprecated
openbabel chemical toolbox Chemistry http://openbabel.org
openblas optimized BLAS library Libraries http://openblas.net
opencl opencl headers Libraries http://khronos.org
openconnect VPN client Internet http://www.infradead.org/openconnect
opencv Open Source Computer Vision Library Libraries http://opencv.org
openexr High dynamic-range image file format Graphics http://www.openexr.com
openmm toolkit for molecular simulation Molecular Biology http://simtk.org
openmpi high performance message passing library Programming Tools http://www.openmpi.org
openms LC/MS data management and analyses Chemistry http://open-ms.sourceforge.net
opera optimal genome scaffolding program Bioinformatics http://sourceforge.net/projects/operasf
orca quantum chemistry Chemistry http://www.thch.uni-bonn.de/tc/orca
orthodb database of orthologs Bioinformatics http://orthodb.org
orthomcl ortholog groups of protein sequences Bioinformatics http://orthomcl.org
ortools Google's software suite for combinatorial optimization Libraries http://developers.google.com/optimizations
ovito scientific visualization and analysis software for atomistic simulation data Graphics http://ovito.org
p3dfft parallel three-dimensional fast Fourier transforms Libraries http://code.google.com/p/p3dfft
p4est Parallel AMR on forests of octrees Libraries http://p4est.org
p7zip file archiver System Tools http://p7zip.sourceforge.net
packmol packing optimization for molecular dynamics simulations Chemistry http://www.ime.unicamp.br/~martinez/packmol
paml phylogenetic analysis by maximum likelihood Bioinformatics http://abacus.gene.ucl.ac.uk
pamlx phylogenetic analysis by maximum likelihood Bioinformatics http://abacus.gene.ucl.ac.uk/software/paml.html
pandoc universal document converter Accessories http://pandoc.org
pango library for laying out and rendering of text, with an emphasis on internationalization Libraries http://www.pango.org
parallel shell tool for executing jobs in parallel System Tools http://www.gnu.org/software/parallel
paraview an open-source, multi-platform data analysis and visualization application Graphics http://www.paraview.org
pbcore Python APIs for interacting with PacBio data files Bioinformatics http://github.com/PacificBiosciences/pbcore
pbh5tools swiss-army knife for interrogating PacBio HDF5 files Bioinformatics http://github.com/PacificBiosciences/pbh5tools
pbsuite automated pipeline to align long sequencing reads to high-confidence draft assembles Bioinformatics http://sourceforge.net/p/pb-jelly
pccalc calculates principal components for datasets with large sample sizes Bioinformatics http://ccge.medschl.cam.ac.uk/software/pccalc
pcre Perl Compatible Regular Expressions Libraries http://www.pcre.org
pdbdagcon sequence consensus Bioinformatics http://github.com/PacificBiosciences/pbdagcon
peaksplitter subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks Bioinformatics http://www.ebi.ac.uk/research/bertone/software
pear Illumina paired-end read and merger Bioinformatics http://sco.h-its.org/exelixis/web/software/pear
pecnv C++ tools for calling structural variants from PE mapping of short reads Bioinformatics http://github.com/molpopgen/pecnv
perf profiling with performance counters Programming Tools http://perf.wiki.kernel.org
perl Perl programming language Programming Tools http://www.perl.org
perl-modules perl modules Libraries http://www.cpan.org
petsc portable, extensible toolkit for scientific computation Mathematics http://www.mcs.anl.gov/petsc
petsc4py PETSc for python Mathematics http://pypi.python.org/pypi/petsc4py
pgplot plotting library for fortran (gfortran 5.2.0) Libraries http://www.astro.caltech.edu/~tjp/pgplot/
pgx parallel graph analytics Computer Science http://www.oracle.com
phantomjs Headless WebKit scriptable with a JavaScript API Internet http://phantomjs.org
photoscan Commercial Photogrammetry software - bring your own license Data Analysis http://www.agistoft.com
php general-purpose scripting language Internet http://php.net
phylocsf determine whether multi-species nucleotide alignment is likely to represent protein-coding region Bioinformatics http://github.com/mlin/PhyloCSF
picard Java-based command-line utilities to manipulate SAM files Bioinformatics http://picard.sourceforge.net
picrust a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes Bioinformatics http://picrust.github.io
pigz parallel implementation of gzip System Tools http://zlib.net/pigz
pin binary instrumentation tool Programming Tools http://software.intel.com/en-us/articles/pintool-downloads
pindel detection of breakpoints of deletions, insertions, inversions, duplications, and other structural variants Bioinformatics http://trac.nbic.nl/pindel
pipipes piRNA pipeline collection developed in Zamore Lab Bioinformatics http://github.com/bowhan/piPipes
pixman a low-level software library for pixel manipulation Libraries http://www.pixman.org
plink whole genome association analysis toolset Bioinformatics http://www.cog-genomics.org/plink2
plumed open source library for free energy calculations Chemistry http://plumed.org
pmw toolkit for building high-level compound widgets in Python using the Tkinter module Libraries http://pmw.sourceforge.net
popbam population-based analyses of next-generation sequencing data Bioinformatics http://sourceforge.net/projects/popbam
popoolation compare allele frequencies for SNPs between two or more populations Bioinformatics http://sourceforge.net/projects/popoolation2
poreseq error correction and variant calling algorithm for nanopore sequencing Bioinformatics http://github.com/tszalay/poreseq
poretools toolkit for working with nanopore sequencing data from Oxford Nanopore Bioinformatics http://poretools.readthedocs.io
praat phonetics by computer Computer Science http://fon.hum.uva.nl/praat
probabel tools for genome-wide association analysis of imputed genetic data Bioinformatics http://genable.org/packages/ProbABEL
progressivecactus multiple genome aligner Bioinformatics https://github.com/glennhickey/progressiveCactus
proovread PacBio hybrid error correction through iteractive short read consensus Bioinformatics http://github.com/BioInf-Wuerzburg/proovread
protobuf language neutral, platform neutral extensible mechanism for serializing structured data Programming Tools http://developers.google.com/protocol-buffers
provide program for viral diversity estimation Bioinformatics http://metagenomics.atc.tcs.com/binning/ProViDE
psfj automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations Graphics http://www.knoplab.de/psfj
psi4conda open-source quantum chemistry Chemistry http://www.psicode.org
pt3 analysis of time-resolved photon counting from PicoHarp 300 T3 mode files Chemistry http://circ.rochester.edu
pybedtools wrapper for BEDTools Bioinformatics http://pypi.python.org/pypi/pybedtools
pycifrw CIF/STAR file support for Python Chemistry http://pypi.python.org/pypi/PyCifRW
pycogent software library for genomic biology Bioinformatics http://pycogent.org
pycuda CUDA wrapper for python Programming Tools http://pypi.python.org/pypi/pycuda
pyfasta fast, memory-efficient, pythonic access to fasta sequence files Bioinformatics http://pypi.python.org/pypi/pyfasta
pymol molecular visualization system on an open-source foundation Graphics http://www.pymol.org
pyqtgraph python graphics and GUI utility Graphics http://pyqtgraph.org
pysam python interface for SAM/BAM sequence alignment and mapping format Bioinformatics http://code.google.com/p/pysam
pysamstats Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file Bioinformatics http://github.com/alimanfoo/pysamstats
pyslurm Python interface to slurm 15.08.8 Libraries https://github.com/PySlurm
pytables python package for managing hierarchical datasets Libraries http://www.pytables.org
python Python programming language Programming Tools http://www.python.org
python3 Python3 programming language Programming Tools http://www.python.org
pyvcf variant call format reader Bioinformatics http://github.com/jamescasbon/PyVCF
pyxaid PYthon eXtension for Ab Initio Dynamics Chemistry http://www.acsu.buffalo.edu/~alexeyak/pyxaid/overview.html
qctool quality control and analysis of gwas datasets Bioinformatics http://www.well.ox.ac.uk/~gav/qctool
qdmr quantitative differentially methylated region Bioinformatics http://bioinfo.hrbmu.edu.cn/qdmr
qe electronic-structure calculations Chemistry http://www.quantum-espresso.org
qgis geographic information system Libraries http://qgis.org
qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram Mathematics http://www.qhull.org
qiime Quantitative Insights into Microbial Ecology Molecular Biology http://qiime.org
qiimetomaaslin convert Qiime output to MaAsLin input Bioinformatics http://bitbucket.org/biobakery/qiimetomaaslin
qrupdate Fortran library for fast updates of QR and Cholesky decompositions. Libraries http://sourceforge.net/projects/qrupdate
qt cross-platform application and UI framework for developers using C++ or QML Libraries http://qt-project.org
qtwebkit Qt port of WebKit Libraries http://trac.webkit.org/wiki/QtWebKit
quast QUality ASessment Tool for Genome Assemblies Bioinformatics http://github.com/ablab/quast
r free software environment for statistical computing and graphics Data Analysis http://www.r-project.org
raxml randomized axelerated maximum likelihood Bioinformatics http://sco.h-its.org/exelixis/web/software/raxml
readline readline utility Libraries http://www.gnu.org
realpath list contents of directories in a tree-like format System Tools http://linux.die.net/man/1/realpath
recon de novo algorithm for identification of repeat families from biological sequences Bioinformatics http://www.genetics.wustl.edu/eddy/recon
repdenovo construct repeats directly from raw reads Bioinformatics http://github.com/Reedwarbler/REPdenovo
repeatmasker program that screens DNA sequences for interspersed repeats and low complexity DNA sequences Bioinformatics http://www.repeatmasker.org
repeatmodeler RepeatModeler is a de-novo repeat family identification and modeling package Bioinformatics http://repeatmasker.org
resqc RNA-seq quality control package Bioinformatics http://rseqc.sourceforge.net
retroseq discovery and genotyping of transposable element variants Bioinformatics http://github.com/tk2/RetroSeq/releases
rh6 RHEL6 packages System Tools http://redhat.com
rmagick Ruby+ImageMagick Libraries http://rmagick.github.io
rmats multivariate analysis of transcript splicing Bioinformatics http://rnaseq-mats.sourceforge.net
rmblast RepeatMasker compatible version of the standard NCBI BLAST suite Bioinformatics http://www.repeatmasker.org/RMBlast.html
rna-star spliced transcripts alignment to a reference Bioinformatics http://code.google.com/p/rna-star
rnastructure RNA and DNA secondary structure prediction and analysis Bioinformatics http://rna.urmc.rochester.edu/RNAstructure.html
rodeo A native Python IDE for Data Science Data Analysis http://rodeo.yhat.com
root A modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R Data Analysis http://root.cern.ch
rsem RNA-Seq by expectation maximization Bioinformatics http://dewlab.biostat.wisc.edu/rsem
rstudio GUI for R Data Analysis http://rstudio.com
ruby dynamic, open source programming language with a focus on simplicity and productivity Programming Tools http://ruby-lang.org
sage open-source mathematics software system Mathematics http://sagemath.org
salmon highly accurate and wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments Bioinformatics http://github.com/COMBINE-lab/salmon
sambamba Tools for working with SAM/BAM data Bioinformatics http://github.com/lomereiter/sambamba
samblaster samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Bioinformatics http://github.com/GregoryFaust/samblaster
samstat displays various properties of next-generation sequencing reads stored in SAM/BAM format Bioinformatics http://sourceforge.net/projects/samstat
samtools utilities for sequence alignments Bioinformatics http://samtools.sourceforge.net
sas data management Data Analysis http://www.sas.com
sbt an open source build tool for Scala and Java projects, similar to Javas Maven or Ant. Programming Tools http://www.scala-sbt.org
scala an object-functional programming and scripting language for general software applications Programming Tools http://www.scala-lang.org
scarpa stand-alone scaffolding tool for NGS data Bioinformatics http://compbio.cs.toronto.edu/hapsembler/scarpa.html
schrodinger computational chemistry package Chemistry http://schrodinger.com
scilab numerical computation Mathematics http://www.scilab.org
scipy open source library of scientific tools Libraries http://scipy.org
scons software construction tool Programming Tools http://www.scons.org
screen window manager Accessories http://gnu.org
selectiontools Pipeline to take VCF through to Selection Analysis Bioinformatics http://github.com/MerrimanLab/selectionTools
sendemail sending SMTP mail from command line System Tools http://caspian.dotconf.net/menu/Software/SendEmail
seqclean sequence cleaner Bioinformatics http://seqclean.sourceforge.net
seqtk toolkit for processing sequences in FASTA/Q formats Bioinformatics http://github.com/lh3/seqtk
sga string graph assembler Bioinformatics http://github.com/jts/sga
shapeit estimation of haplotypes Bioinformatics http://mathgen.stats.ox.ac.uk/genetic_software/shapeit/shapeit.html
shm a powerful seismic waveform analysis tool Physics http://www-seismic-handler.org
shrimp SHort Read Mapping Package Bioinformatics http://compbio.cs.toronto.edu/shrimp
siesta electronic structure calculations Chemistry http://www.icmab.es/siesta
singularity containers System Tools http://singularity.lbl.gov
slicer visualization and medical image computing Graphics http://slicer.org
slurm Slurm job scheduler System Tools http://slurm.schedmd.com/
smartgit SmartGit is a Git client with Mercurial and Subversion support. SmartGit is free for non-commercial use and runs on Mac OS X, Windows and Linux. Programming Tools http://www.syntevo.com/smartgit/
smufin somatic mutation finder Bioinformatics http://cg.bsc.ed/smufin
snappy fast compressor/decompressor System Tools http://github.com/google/snappy
snptest analysis of single SNP association Bioinformatics http://mathgen.stats.ox.ac.uk/genetics_software/snptest/snptest.html
soapdenovo a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds Libraries http://soap.genomics.org.cn/index.html
sopra assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD Bioinformatics http://www.physics.rutgers.edu/~anirvans/SOPRA
sourcetracker Bayesian approach to estimating proportion of a novel community from a set of source environments Bioinformatics http://sourceforge.net/projects/sourcetracker
soxr resampler library Libraries http://sourceforge.net/p/soxr
spades genome assembler Bioinformatics http://bioinf.spbau.ru/spades
sparc sparsity-based consensus algorithm for long erroneous sequencing reads Bioinformatics http://github.com/yechengxi/Sparc
spark a fast and general-purpose cluster computing system System Tools http://spark.apache.org
sparsehash extremely memory-efficient hash_map implementation Programming Tools http://code.google.com/p/sparsehash
sphinx tool that makes it easy to create intelligent and beautiful documentation Libraries http://sphinx-doc.org
splicegrapher prediction of alternative splicing patterns Bioinformatics http://sourceforge.net/projects/splicegrapher
sqlcipher database encryption for SQLite Data Analysis http://sqlcipher.net
sqlite SQL database engine Data Analysis http://www.sqlite.org
sqliteman sqlite3 admin tool Data Analysis http://sourceforge.net/projects/sqliteman
sqliteodbc odbc wrapper for sqlite Data Analysis http://www.ch-werner.de/sqliteodbc
sratoolkit access data from sequence read archive Bioinformatics http://www.ncbi.nlm.nih.gov/books/NBK158900
stack Haskell tool stack Programming Tools http://haskellstack.org
stampy mapping of short reads onto a reference genome Bioinformatics http://www.well.ox.ac.uk/project-stampy
stata data analysis and statistics Data Analysis http://www.stata.com
stride integrates string and de Bruijn graph by decomposing reads within error-prone regions Bioinformatics http://github.com/ythuang0522/StriDe
stringtie transcript assembly and quantification for RNA-seq Bioinformatics http://ccb.jhu.edu/software/stringtie
subversion open source version control system Programming Tools http://subversion.apache.org
suitesparse suite of sparse matrix algorithms Libraries http://www.cise.ufl.edu/research/sparse/SuiteSparse/
sundials suite of nonlinear and differential/algebraic equation solvers Mathematics http://computation.llnl.gov/projects/sundials-suite-nonlinear-differential-algebraic-equation-solvers/sundials-software
swig interface compiler Programming Tools http://www.swig.org
tabix utilities for SAMtools Bioinformatics http://sourceforge.net/projects/samtools/files/tabix
taco multi-sample transcriptome assembly from RNA-seq Bioinformatics http://tacorna.github.io
tandem X! Tandem spectrum modeler Chemistry http://www.thegpm.org/tandem
tar create archives System Tools http://www.gnu.org/software/tar
tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language Programming Tools http://www.tcl.tk/
tclap templatized C++ command line parser Programming Tools http://sourceforge.net/projects/tclap
tcllib The Tcl Library is a kitchen sink of packages across a broad spectrum of things Libraries http://core.tcl.tk/tcllib/home
temp detecting transposable elements, insertions and absences from pooled high-throughput sequencing data Bioinformatics http://github.com/JialiUMassWengLab/TEMP
texinfo official documentation format of the GNU project System Tools http://www.gnu.org/software/texinfo/
texlive TeX document production system Accessories https://www.tug.org/texlive/
tiff TIFF Library and Utilities Libraries http://www.remotesensing.org/libtiff/
tinker molecular mechanics and dynamics with special features for biopolymers Molecular Biology http://dasher.wustl.edu/tinker
tk Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches Programming Tools http://www.tcl.tk/
tmux terminal multiplexer System Tools https://tmux.github.io
tophat fast splice junction mapper for RNA-Seq reads Bioinformatics http://tophat.cbcb.umd.edu
torch scientific computing framework for luajit Programming Tools https://github.com/torch
toyz Toyz for Data Analysis and Reduction Data Analysis https://github.com/fred3m/toyz
transdecoder find coding regions within transcripts Bioinformatics http://transdecoder.github.io
tree list contents of directories in a tree-like format System Tools http://linux.die.net/man/1/tree
trf Tandem Repeats Finder Bioinformatics http://tandem.bu.edu/trf/trf.html
trimgalore quality and adaptor trimming for RRBS or standard FastQ files Bioinformatics http://www.bioinformatics.babraham.ac.uk
trimmomatic flexible read trimming tool for Illumina NGS data Bioinformatics http://www.usadellab.org/cms/index.php?page=trimmomatic
trinityrnaseq RNA-seq de novo assembly Bioinformatics http://trinityrnaseq.sourceforge.net
turbovnc offshoot of TightVNC that accelerates the Tight and JPEG encoding paths of the latter, in part by taking advantage of libjpeg-turbo, a SIMD-accelerated version of libjpeg System Tools http://sourceforge.net/projects/virtualgl/files/TurboVNC
ucsc genome browser command-line tools Bioinformatics http://genome.ucsc.edu
unicycler hybrid assembly pipeline for bacterial genomes Bioinformatics http://github.com/rrwick/Unicycler
unison file synchronization System Tools http://www.cis.upenn.edu/~bcpierce/unison
unixodbc open specification for data sources Data Analysis http://www.unixodbc.org
unrar archive manager System Tools http://www.rarlab.com
unzip ZIP extraction Accessories http://www.linuxfromscratch.org/blfs/view/svn/general/unzip.html
valgrind debugging and profiling Programming Tools http://valgrind.org
vardict sensitive variant called for both single and paired sample variant calling from BAM files Bioinformatics http://github.com/AstraZeneca-NGS/VarDict
varianttools software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis Bioinformatics http://github.com/vatlab/VariantTools
varscan variant detection in next-generation sequencing data Bioinformatics http://sourceforge.net/projects/varscan
vcflib simple C++ library for parsing and manipulating VCF files Bioinformatics http://github.com/ekg/vcflib
vcftools package for working with VCF files Bioinformatics http://vcftools.sourceforge.net
vdjer B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data Bioinformatics http://github.com/mozack/vdjer
velvet sequence assembler for very short reads Bioinformatics http://www.ebi.ac.uk/~zerbino/velvet
velvetoptimiser Perl script for automatically optimizing the three primary parameter optinos for the velvet de novo sequence assembler Bioinformatics http://bioinformatics.net.au/software.velvetoptimiser.shtml
vicare implementation of Scheme language compliant with R6RS standard with several language extensions Programming Tools http://marcomaggi.github.io/vicare.html
vienna prediction and comparison of RNA secondary structures Bioinformatics http://www.tbi.univie.ac.at/RNA
virtualgl OpenGL interposer that allows applications to use remote display hardware Libraries http://www.virtualgl.org
virusseq detection of known viruses and integration sites Bioinformatics http://odin.mdacc.tmc.edu/~xsu1/VirusSeq.html
visit Open Source, interactive, scalable, visualization, animation and analysis tool Graphics https://wci.llnl.gov/codes/visit/
visualsfm GUI application for 3D reconstruction using structure from motion Graphics http://ccwu.me/vsfm
vmd visual molecular dynamics Graphics http://www.ks.uiuc.edu/Research/vmd
volview open-source, intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data Graphics http://www.kitware.com/opensource/volview.html
voro Voronoi diagram Mathematics http://math.lbl.gov/voro++
votca VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge and exciton transport in disordered semiconductors. Its C++ core is interfaced to bash and perl flow-control scripts Molecular Biology http://votca.org
vpnc virtual private network consortium Internet http://vpnc.org
vtk visualization toolkit Graphics http://vtk.org
vxl collection of C++ libraries designed for computer vision research and implementation Libraries http://vxl.sourceforge.net
wannier90 maximally-localized Wannier functions Chemistry http://www.wannier.org
waveplot visualization of results fom DFTB+ Chemistry http://dftb-plus.info
weblogo create sequence logos Bioinformatics http://weblogo.berkeley.edu
weka machine learning algorithms for data mining Data Analysis http://www.cs.waikato.ml/ml/weka
westpa The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis Molecular Biology http://westpa.github.io
wgs whole-genome shotgun assembler Bioinformatics http://sourceforge.net/projects/wgs-assembler
wine compatibility layer for Windows apps - 32 bit System Tools http://winehq.org
wx cross-platform GUI library Libraries http://www.wxwidgets.org
wxPython a blending of the wxWidgets C++ class library with the Python programming language Libraries http://www.wxpython.org
wxwidgets cross-platform GUI library Programming Tools http://wxwidgets.org
x-devel X windows devel pkgs Libraries http://www.x.org
xblas eXtended precision Basic Linear Algebra Subroutines Libraries http://www.netlib.org/xblas
xcb X protocol C-language Binding (XCB) Libraries http://xcb.freedesktop.org
xcrysden X-window CRYstalline Structures and DENsities Chemistry http://www.xcrysden.org
xdmf Extensible Data Module and Format, a data model, library and file format for storing and managing data Libraries http://xdmf.org/index.php/Main_Page
xerces-c XML parser Programming Tools http://xerces.apache.org
xls2csv converts xsl files to csv - perl version System Tools http://search.cpan.org/~ken/xls2csv-1.07/script/xls2csv
xpdf PDF viewer Accessories http://www.foolabs.com/xpdf
xterm Xwindow terminal System Tools http://invisible-island.net/xterm
xz free general-purpose data compression software with high compression ratio Libraries http://tukaani.org/xz/
yaehmop Yet Another extended Huckel Molecular Orbital Package Chemistry http://yaehmop.sourceforge.net
yasm Yasm assembler Programming Tools http://yasm.tortall.net
zint barcode generator Libraries http://sourceforge.net/projects/zint
zlib Compression Library Libraries http://zlib.net
zmq ZeroMQ lightweight messaging kernel Libraries https://github.com/zeromq/libzmq